I'm running a single main boot drive for windows, which I'm planning on reformatting. Also connected to the computer are 2 1TB drives in RAID 1 that I use for storage. The RAID 1 is established by "Intel Matrix Storage Manager" (my raid controller is integrated on the motherboard, which is a 975xbx). If I format my main drive to reinstall windows will the raid essentially be reset? Or is the RAID controlled such that a format of a drive separate from the RAID would not effect it?
The headers of RAID configuration is written as part of the disks in the array and not part of the OS. So reformatting the drive which OS is installed on will not affect your RAID array.
If you've set SATA mode to 'RAID' in BIOS and don't provide additional driver during OS installation then Windows should detect only the non-RAID'ed drive(s).
After Windows has been installed then install Intel Matrix RAID software/driver to recognise the RAID1 array (with all data intacted).
That's with Vista/Win7. With XP you'll have to supply driver for ICH7R RAID.